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    Yorodumi
    - EMDB-1484: Ribosome Binding of a Single Copy of the SecY Complex: Implicatio... -

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    Basic information

    Entry
    Database: EMDB / ID: 1484
    TitleRibosome Binding of a Single Copy of the SecY Complex: Implications for Protein Translocation
    Keywordsribosome / secY / translocation / electron microscopy
    SampleRibosome SecY complex
    SourceEscherichia coli / bacteria /
    Map dataEscherichia coli ribosome secY complex
    Methodsingle particle reconstruction, at 9.6 A resolution
    AuthorsMenetret JF / Schaletzky J / Clemons WM Jr / Osborne AR / Skanland SS / Denison C / Gygi SP / Kirkpatrick DS / Park E / Ludtke SJ / Rapoport TA / Akey CW
    CitationMol. Cell, 2007, 28, 1083-1092

    Mol. Cell, 2007, 28, 1083-1092 StrPapers
    Ribosome binding of a single copy of the SecY complex: implications for protein translocation.
    Jean-François Ménétret / Julia Schaletzky / William M Clemons / Andrew R Osborne / Sigrid S Skånland / Carilee Denison / Steven P Gygi / Don S Kirkpatrick / Eunyong Park / Steven J Ludtke / Tom A Rapoport / Christopher W Akey

    DateDeposition: Feb 26, 2008 / Header (metadata) release: Feb 26, 2008 / Map release: May 29, 2009 / Last update: Feb 26, 2008

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1.5
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by height
    • Surface level: 1.5
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-3bo0
    • Surface level: 1.5
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view with fitted model
    • Atomic models: : PDB-4v7i
    • Surface level: 1.5
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1484.map.gz (map file in CCP4 format, 11665 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    144 pix
    2.73 A/pix
    = 393.12 A
    144 pix
    2.73 A/pix
    = 393.12 A
    144 pix
    2.73 A/pix
    = 393.12 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.73 A
    Density
    Contour Level:0.95 (by author), 1.5 (movie #1):
    Minimum - Maximum-4.99671 - 10.6495
    Average (Standard dev.)0.149684 (0.868322)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions144144144
    Origin-72-72-72
    Limit717171
    Spacing144144144
    CellA=B=C: 393.12 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.732.732.73
    M x/y/z144144144
    origin x/y/z0.0000.0000.000
    length x/y/z393.120393.120393.120
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-55-55-55
    NX/NY/NZ111111111
    MAP C/R/S123
    start NC/NR/NS-72-72-72
    NC/NR/NS144144144
    D min/max/mean-4.99710.6490.150

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    Supplemental data

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    Sample components

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    Entire Ribosome SecY complex

    EntireName: Ribosome SecY complex / Number of components: 1 / Oligomeric State: monomer
    MassTheoretical: 3.2 MDa

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    Component #1: ribosome-prokaryote, 70S ribosome

    Ribosome-prokaryoteName: 70S ribosome / a.k.a: ribosome / Prokaryote: ALL / Recombinant expression: No
    MassTheoretical: 3.2 MDa
    SourceSpecies: Escherichia coli / bacteria /

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.3 mg/ml
    Buffer solution: 50mM Hepes-KOH, 100mM KOAc, 10mM Mg(OAc)2, 0.05% DDM
    pH: 7.5
    Support film400 mesh Cu grids with continuous carbon film
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 95 % / Method: 1 second blot / Details: Vitrification instrument: home-made

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 20
    Details: About 30 percent of the data were collected at 30 degree tilt and micrographs were processed in small strips parallel to the tilt axis to correct for the defocus ramp.
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 51000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm
    Specimen HolderHolder: eucentric / Model: GATAN LIQUID NITROGEN / Tilt Angle: 0 - 30 deg. / Temperature: 90 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 351 / Scanner: OTHER / Sampling size: 4.5 microns / Bit depth: 16 / OD range: 1 / Details: Creoscitex Eversmart scanner was used

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 39000 / Details: 1900 classes were used in EMAN 3D refinement / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: projection matching / Software: EMAN / CTF correction: by micrograph / Resolution: 9.6 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: coot / Refinement protocol: rigid body / Refinement space: REAL
    Details: Protocol: manual in O and Chimera. Loop geometry was regularized in Coot.
    Input PDB model: 1RHZ, 2I2T, 2I2P
    Output model

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